Matthew Stephens, Ph.D.


Research Description

My general interests include Bayesian and computational statistics, particularly when applied to problems in population genetics.  Specific interests include:

  • Estimating haplotypes from population genotype data (for which I distribute a software package PHASE).
  • Developing statistical models for patterns of linkage disequilibrium across multiple loci, and using these patterns to identify recombination hotspots.
  • Spatial modelling of allele frequency variation.

Selected Publications

Promoter shape varies across populations and affects promoter evolution and expression noise.
Schor IE, Degner JF, Harnett D, Cannavo E, Casale FP, Shim H, Garfield DA, Birney E, Stephens M, Stegle O, Furlong EE
(2017 Apr) Nat Genet. 2017 Apr;49(4):550-558. doi: 10.1038/ng.3791. Epub 2017 Feb 13. 28191888

False discovery rates: a new deal.
Stephens M
(2017 Apr) Biostatistics. 2017 Apr 1;18(2):275-294. doi: 10.1093/biostatistics/kxw041. 27756721 (Full Text)

Visualizing the structure of RNA-seq expression data using grade of membership models.
Dey KK, Hsiao CJ, Stephens M
(2017 Mar) PLoS Genet. 2017 Mar 23;13(3):e1006599. doi: 10.1371/journal.pgen.1006599. eCollection 2017 Mar. 28333934 (Full Text)

Variance adaptive shrinkage (vash): flexible empirical Bayes estimation of variances.
Lu M, Stephens M
(2016 Nov) Bioinformatics. 2016 Nov 15;32(22):3428-3434. Epub 2016 Jul 19. 27436563 (Full Text)

Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling.
Raj A, Wang SH, Shim H, Harpak A, Li YI, Engelmann B, Stephens M, Gilad Y, Pritchard JK
(2016 May) Elife. 2016 May 27;5. pii: e13328. doi: 10.7554/eLife.13328. 27232982 (Full Text)

Visualizing spatial population structure with estimated effective migration surfaces.
Petkova D, Novembre J, Stephens M
(2016 Jan) Nat Genet. 2016 Jan;48(1):94-100. doi: 10.1038/ng.3464. Epub 2015 Dec 7. 26642242 (Full Text)

A Simple Model-Based Approach to Inferring and Visualizing Cancer Mutation Signatures.
Shiraishi Y, Tremmel G, Miyano S, Stephens M
(2015 Dec) PLoS Genet. 2015 Dec 2;11(12):e1005657. doi: 10.1371/journal.pgen.1005657. eCollection 2015 Dec. 26630308 (Full Text)

Efficient multivariate linear mixed model algorithms for genome-wide association studies.
Zhou X, Stephens M
(2014 Apr) Nat Methods. 2014 Apr;11(4):407-9. doi: 10.1038/nmeth.2848. Epub 2014 Feb 16. 24531419 (Full Text)

Polygenic modeling with bayesian sparse linear mixed models.
Zhou X, Carbonetto P, Stephens M
(2013) PLoS Genet. 2013;9(2):e1003264. doi: 10.1371/journal.pgen.1003264. Epub 2013 Feb 7. 23408905 (Full Text)

A unified framework for association analysis with multiple related phenotypes.
Stephens M
(2013) PLoS One. 2013 Jul 5;8(7):e65245. doi: 10.1371/journal.pone.0065245. Print 2013. 23861737 (Full Text)

A statistical framework for joint eQTL analysis in multiple tissues.
Flutre T, Wen X, Pritchard J, Stephens M
(2013 May) PLoS Genet. 2013 May;9(5):e1003486. doi: 10.1371/journal.pgen.1003486. Epub 2013 May 9. 23671422 (Full Text)

Statistical inference of transmission fidelity of DNA methylation patterns over somatic cell divisions in mammals.
A Q Fu, D P Genereux, R Stoger, C D Laird, and M Stephens.
Annals of Applied Statistics 4(2): 871-892, June 2010.

A nested mixture model for protein identification using mass spectrometry.
Q Li, M MacCoss, and M Stephens.
Annals of Applied Statistics 4(2): 962-987, June 2010

Using linear predictors to impute allele frequencies from summary or pooled genotype data.
X Wen and M Stephens
Annals of Applied Statistics 4(3): 1158-1182, September 2010

Analysis of population structure: a unifying framework and novel methods based on sparse factor analysis.
B E Engelhardt, and M Stephens
PLoS Genetics 6(9): e1001117. Software

Understanding mechanisms underlying human gene expression variation with RNA sequencing.
J K Pickrell, J C Marioni, A A Pai, J F Degner, B E Engelhardt, E Nkadori, J B Veyrieras, M Stephens, Y Gilad, and J K Pritchard
Nature, 464(7289):768-72, Mar 2010

Genome-wide association of lipid-lowering response to statins in combined study populations
M J Barber, L M Mangravite, C L Hyde, D I Chasman, J D Smith, C A McCarty, X Li, R A Wilke, M J Rieder, P T Williams, P M Ridker, A Chatterjee, J I Rotter, D A Nickerson, M Stephens, R M Krauss
PLoS ONE, Mar 2010 Supplementary results data page

Bayesian statistical methods for genetic association studies.
M Stephens and D J Balding
Nat Rev Genet, 10(10):681-90, Oct 2009

Practical issues in imputation-based association mapping.
Y Guan and M Stephens
PLoS Genet, 4(12), Dec 2008

Genes mirror geography within Europe.
J Novembre, T Johnson, K Bryc, Z Kutalik, A R Boyko, A Auton, A Indap, KS King, S Bergmann, M R Nelson, M Stephens, and C D Bustamante
Nature, 456(7218):98-101, Nov 2008

High-resolution mapping of expression-QTLs yields insight into human gene regulation.
J B Veyrieras, S Kudaravalli, S Y Kim, E T Dermitzakis, Y Gilad, M Stephens, and J K Pritchard
PLoS Genet, 4(10), Oct 2008

Combating the illegal trade in African elephat ivory with DNA forensics.
S K Wasser, W J Clark, O Drori, E S Kisamo, C Mailand, B Mutayoba, and M Stephens
Conserv Biol, 22(4):1065-1071, Aug 2008

RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays.
J C Marioni, C E Mason, S M Mane, M Stephens, and Y Gilad
Genome Res, 18(9):1509-1517, Sep 2008

Linkage disequilibrium-based quality control for large-scale genetic studies.
P Scheet and M Stephens
PLoS Genet, 4(8), 2008

Polymorphisms of the HNF1A gene encoding hepatocyte nuclear factor-1 alpha are accosicated with c-reactive protein.
A P Reiner, M J Barber, Y Guan, P M Ridkerm L A Lange, D I Chasman, J D Walston, G M Cooper, N S Jenny, M J Rieder, J P Durda, J D Smith, J Novembre, R P Tracy, J I Rotter, M Stephens, D A Nickerson, and R M Krauss
Am J Hum Genet., 82(5):1193-1201, May 2008

Interpreting principal component analyses of spatial population genetic variation.
J Novembre and M Stephens
Nat Genet, 40(5):646-649, May 2008

Imputation-based analysis of association studies: candidate regions and quantitative traits.
B Servin and M Stephens
PLoS Genet, 3(7), Jul 2007

Using DNA to track the origin of the largest ivory seizure since the 1989 trade ban.

S K Wasser, C Mailand, R Booth, B Mutayoba, E Kisamo, B Clark, and M Stephens

Proc Natl Acad Sci U S A, 104(10):4228-4233, Mar 2007